I was repeating this quest line for somachords just recently.
I wasn't able to get any somachords from the 1st mission. I even tried aborting the mission and retrying. And no somachords in 1st mission. The same behavior occurred on other missions as well; no somachords, but i did find cephalon fragments.
I don't remember exactly how many times I played those missions, but I did quest line 4-6 times and individual missions were aborted and replayed almost 10 times per quest line, until in the 4th mission I found 1st somachord apparently in random location. After that no somachords in the rest of the quest line, but in the new quest line the rest somachords were exactly where they should be.
For me it looks like getting 1st fragment is bugged; It does not appear where it should be, or there is way too low roll chance for it to appear. If you are lucky/persistent enough you can find it in random cephalon location throughout the rest of the quest line.